From aed7840d4fa5c5e2d47c6928608269292bfe00e2 Mon Sep 17 00:00:00 2001
From: mathiasg <mathiasg@stanford.edu>
Date: Tue, 13 Jul 2021 14:44:21 -0400
Subject: [PATCH 1/2] DOC: Display API per module

---
 docs/_api/base.rst      |  6 ++++++
 docs/_api/io.rst        | 39 +++++++++++++++++++++++++++++++++++++++
 docs/_api/linear.rst    |  6 ++++++
 docs/_api/manip.rst     |  6 ++++++
 docs/_api/nonlinear.rst |  6 ++++++
 docs/_api/patched.rst   |  6 ++++++
 docs/api.rst            | 15 +++++++--------
 7 files changed, 76 insertions(+), 8 deletions(-)
 create mode 100644 docs/_api/base.rst
 create mode 100644 docs/_api/io.rst
 create mode 100644 docs/_api/linear.rst
 create mode 100644 docs/_api/manip.rst
 create mode 100644 docs/_api/nonlinear.rst
 create mode 100644 docs/_api/patched.rst

diff --git a/docs/_api/base.rst b/docs/_api/base.rst
new file mode 100644
index 00000000..56482d9a
--- /dev/null
+++ b/docs/_api/base.rst
@@ -0,0 +1,6 @@
+====
+Base
+====
+
+.. automodule:: nitransforms.base
+    :members:
diff --git a/docs/_api/io.rst b/docs/_api/io.rst
new file mode 100644
index 00000000..7666253b
--- /dev/null
+++ b/docs/_api/io.rst
@@ -0,0 +1,39 @@
+===
+IO
+===
+
+Reading and writing of transform files.
+
+--------
+Base I/O
+--------
+.. automodule:: nitransforms.io.base
+    :members:
+
+-----------------
+Tool Specific I/O
+-----------------
+
+^^^^
+AFNI
+^^^^
+.. automodule:: nitransforms.io.afni
+    :members:
+
+^^^
+FSL
+^^^
+.. automodule:: nitransforms.io.fsl
+    :members:
+
+^^^
+ITK
+^^^
+.. automodule:: nitransforms.io.itk
+    :members:
+
+^^^^^^^^^^^^^^
+FreeSurfer/LTA
+^^^^^^^^^^^^^^
+.. automodule:: nitransforms.io.lta
+    :members:
diff --git a/docs/_api/linear.rst b/docs/_api/linear.rst
new file mode 100644
index 00000000..728b2ed0
--- /dev/null
+++ b/docs/_api/linear.rst
@@ -0,0 +1,6 @@
+=================
+Linear Transforms
+=================
+
+.. automodule:: nitransforms.linear
+    :members:
diff --git a/docs/_api/manip.rst b/docs/_api/manip.rst
new file mode 100644
index 00000000..b14f1fd3
--- /dev/null
+++ b/docs/_api/manip.rst
@@ -0,0 +1,6 @@
+=============
+Manipulations
+=============
+
+.. automodule:: nitransforms.manip
+    :members:
diff --git a/docs/_api/nonlinear.rst b/docs/_api/nonlinear.rst
new file mode 100644
index 00000000..ab3574b4
--- /dev/null
+++ b/docs/_api/nonlinear.rst
@@ -0,0 +1,6 @@
+====================
+Nonlinear Transforms
+====================
+
+.. automodule:: nitransforms.nonlinear
+    :members:
diff --git a/docs/_api/patched.rst b/docs/_api/patched.rst
new file mode 100644
index 00000000..b50cb6de
--- /dev/null
+++ b/docs/_api/patched.rst
@@ -0,0 +1,6 @@
+=========================
+Patched Nibabel Functions
+=========================
+
+.. automodule:: nitransforms.patched
+    :members:
diff --git a/docs/api.rst b/docs/api.rst
index 1d87ebd2..2d67b21b 100644
--- a/docs/api.rst
+++ b/docs/api.rst
@@ -3,12 +3,11 @@ Library API (application program interface)
 Information on specific functions, classes, and methods for developers.
 
 .. toctree::
-   :glob:
+   :maxdepth: 1
 
-   api/nitransforms.base
-   api/nitransforms.cli
-   api/nitransforms.io
-   api/nitransforms.linear
-   api/nitransforms.manip
-   api/nitransforms.nonlinear
-   api/nitransforms.patched
\ No newline at end of file
+   _api/base
+   _api/io
+   _api/linear
+   _api/manip
+   _api/nonlinear
+   _api/patched

From d3d8ff84464ca30affa20d0bee00b7d1416807d1 Mon Sep 17 00:00:00 2001
From: mathiasg <mathiasg@stanford.edu>
Date: Tue, 13 Jul 2021 15:10:05 -0400
Subject: [PATCH 2/2] DOC: Add documentation badge to README [skip ci]

---
 README.md | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/README.md b/README.md
index efde9358..f417fd24 100644
--- a/README.md
+++ b/README.md
@@ -4,6 +4,7 @@
 [![codecov](https://codecov.io/gh/poldracklab/nitransforms/branch/master/graph/badge.svg)](https://codecov.io/gh/poldracklab/nitransforms)
 [![doi](https://img.shields.io/badge/doi-10.31219%2Fosf.io%2F8aq7b-blue.svg)](https://doi.org/10.31219/osf.io/8aq7b)
 [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/poldracklab/nitransforms/master?filepath=docs%2Fnotebooks%2F)
+[![Docs](https://readthedocs.org/projects/nitransforms/badge/?version=latest)](http://nitransforms.readthedocs.io/en/latest/?badge=latest)
 
 A development repo for [nipy/nibabel#656](https://github.com/nipy/nibabel/pull/656)
 
@@ -23,6 +24,6 @@ to apply transforms generated by the most popular neuroimaging packages and libr
 (AFNI, FSL, FreeSurfer, ITK, and SPM).
 The proposed software is subject to continuous integration tests to check the
 compatibility with each supported tool after every change to the code base.
-Compatibility between software tools and imaging formats is a necessary bridge 
+Compatibility between software tools and imaging formats is a necessary bridge
 to ensure the reproducibility of results and enable the optimization and evaluation
 of current image processing and analysis workflows.